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Refactored entire NA12878KB to allow us to easily build a na12878kb.j…

…ar for IGV integration

-- Just separated infrastructure into core package, away from the walkers themselves.
-- Added na12878kb.jar target that builds a jar that can run a test main function (see testNA12878kbJar.csh)
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commit 029e6efde2068a18948fe0124f9a87c9c1daad5a 1 parent fe6d413
Mark DePristo authored
Showing with 18 additions and 0 deletions.
  1. +18 −0 build.xml
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18 build.xml
@@ -679,6 +679,24 @@
</jar>
</target>
+ <target name="na12878kb.jar" depends="gatk.compile,init.jar">
+ <jar jarfile="${dist.dir}/na12878kb.jar">
+ <fileset dir="${java.classes}">
+ <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
+ <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
+ <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
+ <include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
+ <include name="org/broadinstitute/sting/utils/Utils.class"/>
+ <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
+ <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
+ <include name="net/sf/picard/reference/FastaSequenceFile.class"/>
+ </fileset>
+ <fileset dir="${java.private.source.dir}">
+ <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
+ </fileset>
+ </jar>
+ </target>
+
<target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
<path refid="gatk.resources"/>
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